Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: kallisto
https://packages.ecosyste.ms/registries/pypi.org/packages/kallisto
The Kallisto software enables the efficient calculation of atomic features that can be used within a quantitative structure-activity relationship (QSAR) approach. Furthermore, several modelling helpers are implemented.
9 versions
Latest release: about 1 year ago
2 dependent packages
282 downloads last month
Papers Mentioning kallisto 307
10.12688/f1000research.15666.3
A systematic performance evaluation of clustering methods for single-cell RNA-seq dataCited by: 33
Author(s): Angelo Duò, Mark D. Robinson, Charlotte Soneson
Software Mentions: 17
Published: about 4 years ago
10.12688/f1000research.15398.3
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantificationCited by: 53
Author(s): Michael I. Love, Charlotte Soneson, Rob Patro
Software Mentions: 16
Published: about 6 years ago
10.1093/bioinformatics/btw777
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in RCited by: 1,059
Author(s): Davis J. McCarthy, Kieran R Campbell, Aaron T. L. Lun, Quin F. Wills
Software Mentions: 14
Published: almost 8 years ago
10.12688/f1000research.8900.2
DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomicsCited by: 105
Author(s): Małgorzata Nowicka, Mark D. Robinson
Software Mentions: 14
Published: almost 8 years ago
10.1186/s12859-021-04142-3
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analysesCited by: 11
Author(s): Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise A Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordóñez, Andrew E. Jaffe, Leonardo Collado‐Torres
Software Mentions: 13
Published: over 3 years ago
10.1186/s13059-020-02151-8
Alignment and mapping methodology influence transcript abundance estimationCited by: 80
Author(s): Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Fatemeh Almodaresi, Charlotte Soneson, Michael I. Love, Carl Kingsford, Rob Patro
Software Mentions: 13
Published: about 4 years ago
10.1038/s42003-021-01941-5
CENP-A overexpression promotes distinct fates in human cells, depending on p53 statusCited by: 23
Author(s): Daniel Jeffery, Alberto Gatto, Katrina Podsypanina, Charlène Renaud-Pageot, Rebeca Ponce Landete, Lorraine Bonneville, Marie Dumont, Daniele Fachinetti, Geneviève Almouzni
Software Mentions: 12
Published: over 3 years ago
10.1371/journal.pone.0190152
RNA-Seq differential expression analysis: An extended review and a software toolCited by: 389
Author(s): Juliana Costa-Silva, Douglas Silva Domingues, Fabrício Martins Lopes
Software Mentions: 12
Published: almost 7 years ago
10.1371/journal.pcbi.1008585
Preprocessing choices affect RNA velocity results for droplet scRNA-seq dataCited by: 43
Author(s): Charlotte Soneson, Avi Srivastava, Rob Patro, Michael Stadler
Software Mentions: 11
Published: almost 4 years ago
10.3390/ijms21218148
Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L.Cited by: 25
Author(s): Stephanie Schaarschmidt, Axel Fischer, Lovely Mae F Lawas, Rejbana Alam, Endang M. Septiningsih, Julia Bailey‐Serres, Krishna Jagadish, Bruno Huettel, Dirk K. Hincha, Ellen Zuther
Software Mentions: 11
Published: about 4 years ago
10.1186/s12859-020-03846-2
ARPIR: automatic RNA-Seq pipelines with interactive reportCited by: 10
Author(s): Giulio Spinozzi, Valentina Tini, Alessia Adorni, Brunangelo Falini, Maria Paola Martelli
Software Mentions: 11
Published: almost 4 years ago
10.1038/s41416-020-0887-6
UGT2B17 modifies drug response in chronic lymphocytic leukaemiaCited by: 12
Author(s): Éric P. Allain, Michèle Rouleau, Katrina Vanura, Sophie Tremblay, Joanie Vaillancourt, Vincent Bat, Patrick Caron, Lyne Villeneuve, Adrien Labriet, Véronique Turcotte, Trang Le, Medhat Shehata, Susanne Schnabl, Dita Demirtas, Rainer Hubmann, Charles Joly-Beauparlant, Arnaud Droit, Ulrich Jäger, Philipp B. Staber, Éric Lévesque, Chantal Guillemette
Software Mentions: 10
Published: over 4 years ago
10.1186/s13073-020-0710-2
Interactions between the gut microbiome and host gene regulation in cystic fibrosisCited by: 65
Author(s): Gargi Dayama, Sambhawa Priya, David Niccum, Alexander Khoruts, Ran Blekhman
Software Mentions: 10
Published: almost 5 years ago
10.7554/eLife.43257
Beta-catenin signaling regulates barrier-specific gene expression in circumventricular organ and ocular vasculaturesCited by: 65
Author(s): Yanshu Wang, Mark F Sabbagh, Xiaowu Gu, Amir Rattner, John Williams, Jeremy Nathans
Software Mentions: 10
Published: over 5 years ago
10.1186/s12859-020-03866-y
Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipelineCited by: 7
Author(s): Yusuf Khan, Daniel Hammarström, Bent R. Rønnestad, Stian Ellefsen, Rafi Ahmad
Software Mentions: 10
Published: almost 4 years ago
10.1186/s13059-021-02337-8
Best practices on the differential expression analysis of multi-species RNA-seqCited by: 36
Author(s): Matthew Chung, Vincent M. Bruno, David A. Rasko, Christina A. Cuomo, José F. Muñoz, Jonathan Livny, Amol Shetty, Anup Mahurkar, Julie C. Dunning Hotopp
Software Mentions: 10
Published: over 3 years ago
10.1186/s13059-021-02360-9
Role of epigenetics in unicellular to multicellular transition in DictyosteliumCited by: 8
Author(s): Simon Yuan Wang, Elizabeth A. Pollina, I‐Hao Wang, Lindsay K. Pino, Henry L. Bushnell, Ken Takashima, Colette Fritsche, George Sabin, Benjamin A. Garcia, Paul L. Greer, Eric Lieberman Greer
Software Mentions: 10
Published: over 3 years ago
10.1128/mBio.00399-21
Salmonella enterica Serovar Typhimurium SPI-1 and SPI-2 Shape the Global Transcriptional Landscape in a Human Intestinal Organoid Model SystemCited by: 12
Author(s): Anna-Lisa E. Lawrence, Basel H. Abuaita, Ryan P. Berger, David R. Hill, Sha Huang, Veda K. Yadagiri, Brooke Bons, Courtney Fields, Christiane E. Wobus, Jason R. Spence, Vincent B. Young, Mary X. O’Riordan
Software Mentions: 9
Published: over 3 years ago
10.7554/eLife.58178
16p11.2 microdeletion imparts transcriptional alterations in human iPSC-derived models of early neural developmentCited by: 24
Author(s): Julien G. Roth, Kristin Muench, Aditya Asokan, Victoria M Mallett, Hongwei Gai, Yogendra Verma, Stephen G. Weber, Carol Charlton, Jonas L. Fowler, Kyle M. Loh, Ricardo E. Dolmetsch, Theo Palmer
Software Mentions: 9
Published: about 4 years ago
10.1534/g3.120.401436
The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid WheatCited by: 18
Author(s): Sophie A Harrington, Anna E Backhaus, Ajit Singh, Keywan Hassani‐Pak, Cristóbal Uauy
Software Mentions: 9
Published: about 4 years ago
10.12688/f1000research.22731.2
Fast analysis of scATAC-seq data using a predefined set of genomic regionsCited by: 10
Author(s): Valentina Giansanti, Ming Tang, Davide Cittaro
Software Mentions: 9
Published: over 4 years ago
10.7554/eLife.39380
Intergenerational epigenetic inheritance of cancer susceptibility in mammalsCited by: 38
Author(s): Bluma J. Lesch, Zuzana Tóthová, Elizabeth A. Morgan, Zhicong Liao, Roderick T. Bronson, Benjamin L. Ebert, David C. Page
Software Mentions: 9
Published: over 5 years ago
10.3390/genes12070995
Effects of the Developmental Regulator BOLITA on the Plant MetabolomeCited by: 3
Author(s): Hugo Gerardo Lazcano-Ramírez, Roberto Gamboa-Becerra, Irving Jair Garcia-Lopez, Ricardo A. Chávez Montes, David Díaz-Ramírez, Octavio Martı́nez de la Vega, José Juan Ordaz-Ortíz, Stefan de Folter, Axel Tiessen-Favier, Robert Winkler, Nayelli Marsch-Martínez
Software Mentions: 9
Published: over 3 years ago
10.1186/s13041-020-00681-7
Brain transcriptome analysis reveals subtle effects on mitochondrial function and iron homeostasis of mutations in the SORL1 gene implicated in early onset familial Alzheimer’s diseaseCited by: 22
Author(s): Karissa Barthelson, Stephen Pederson, Morgan Newman, Michael Lardelli
Software Mentions: 9
Published: about 4 years ago
10.15252/msb.20177862
Comprehensive innate immune profiling of chikungunya virus infection in pediatric casesCited by: 53
Author(s): Daniela Michlmayr, Theodore R. Pak, Adeeb Rahman, El ad David Amir, Eun Young Kim, Seunghee Kim‐Schulze, Maria Suprun, Michael G. Stewart, Guajira P. Thomas, Ángel Balmaseda, Li Wang, Jun Zhu, Mayte Suárez‐Fariñas, Steven M. Wolinsky, Andrew Kasarskis, Eva Harris
Software Mentions: 9
Published: over 6 years ago
10.1128/mSystems.00917-20
FADU: a Quantification Tool for Prokaryotic Transcriptomic AnalysesCited by: 7
Author(s): Matthew Chung, Ricky S. Adkins, John Mattick, Katie R. Bradwell, Amol Shetty, Lisa Sadzewicz, Luke J. Tallon, Claire M. Fraser, David A. Rasko, Anup Mahurkar, Julie C. Dunning Hotopp
Software Mentions: 8
Published: over 3 years ago
10.1038/s41416-020-0851-5
Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell linesCited by: 36
Author(s): Luciane T. Kagohara, Fernando T. Zamunér, Emily F. Davis-Marcisak, Gaurav Sharma, Michael Considine, Jawara Allen, Srinivasan Yegnasubramanian, Daria A. Gaykalova, Elana J. Fertig
Software Mentions: 8
Published: over 4 years ago
10.1038/s41598-020-62354-8
Differential stromal reprogramming in benign and malignant naturally occurring canine mammary tumours identifies disease-modulating stromal componentsCited by: 18
Author(s): Parisa Amini, Sina Nassiri, Alexandra Malbon, Enni Markkanen
Software Mentions: 8
Published: over 4 years ago
10.1038/s42003-020-01377-3
Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal wormCited by: 71
Author(s): Stephen R. Doyle, Alan S. Tracey, Roz Laing, Nancy Holroyd, David J. Bartley, Wojtek Bazant, Helen Beasley, Robin N. Beech, Collette Britton, Karen Brooks, Umer Chaudhry, Kirsty Maitland, Axel Martinelli, Jennifer D. Noonan, Michael Paulini, Michael A. Quail, Elizabeth Redman, Faye H. Rodgers, Guillaume Sallé, Muhammad Zubair Shabbir, Geetha Sankaranarayanan, Janneke Wit, Kevin Howe, Neil Sargison, Eileen Devaney, Matthew Berriman, John S. Gilleard, James A. Cotton
Software Mentions: 8
Published: about 4 years ago
10.1093/gbe/evaa191
Coexpression Clusters and Allele-Specific Expression in Metabolism-Based Herbicide ResistanceCited by: 17
Author(s): Darci A. Giacomini, Eric Patterson, Anita Küpper, Roland Beffa, Todd A. Gaines, Patrick J. Tranel
Software Mentions: 8
Published: about 4 years ago
10.3389/fpls.2018.01625
Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abiesCited by: 9
Author(s): Shirin Akhter, Warren W. Kretzschmar, Veronika Nordal, Nicolas Delhomme, Nathaniel R. Street, Ove Nilsson, Olof Emanuelsson, Jens F. Sundström
Software Mentions: 8
Published: about 6 years ago
10.1186/s13059-020-01998-1
Wheat chromatin architecture is organized in genome territories and transcription factoriesCited by: 89
Author(s): Lorenzo Concia, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Azahara Martin-Ramirez, Ying Huang, Magali Perez, Séverine Domenichini, Natalia Y. Rodriguez Granados, Soon-Kap Kim, Thomas Blein, Susan Duncan, Clement Pichot, Deborah Manza‐Mianza, Caroline Juéry, Etienne Paux, Graham Moore, Heribert Hirt, Catherine Bergounioux, Martín Crespi, Magdy M. Mahfouz, Abdelhafid Bendahmane, Chang Liu, Anthony Hall, Cécile Raynaud, David Latrasse, Moussa Benhamed
Software Mentions: 8
Published: over 4 years ago
10.1242/dmm.040444
Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinomaCited by: 19
Author(s): Parisa Amini, Sina Nassiri, Julia Ettlin, Alexandra Malbon, Enni Markkanen
Software Mentions: 8
Published: almost 6 years ago
10.1186/s13059-015-0862-3
Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usageCited by: 107
Author(s): Charlotte Soneson, Katarina L. Matthes, Małgorzata Nowicka, Charity W. Law, Mark D. Robinson
Software Mentions: 8
Published: almost 9 years ago
10.3390/v12090956
Human Endogenous Retrovirus Expression Is Associated with Head and Neck Cancer and Differential SurvivalCited by: 17
Author(s): Allison R. Kolbe, Matthew L. Bendall, Alexander T. Pearson, Doru Paul, Douglas F. Nixon, Marcos Pérez‐Losada, Keith A. Crandall
Software Mentions: 8
Published: about 4 years ago
10.1186/s13059-019-1921-y
Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysisCited by: 68
Author(s): Rui Yang, Sen Cheng, Nan Luo, Ranran Gao, Kezhuo Yu, Boxi Kang, Li Wang, Qiming Zhang, Fang Qiao, Lei Zhang, Chen Li, Aibin He, Xueda Hu, Jirun Peng, Xianwen Ren, Zemin Zhang
Software Mentions: 8
Published: almost 5 years ago
10.7554/eLife.64919
Tissue-autonomous immune response regulates stress signaling during hypertrophyCited by: 11
Author(s): Robert Krautz, Dilan Khalili, Ulrich Theopold
Software Mentions: 8
Published: almost 4 years ago
10.15252/msb.20198831
The impact of the genetic background on gene deletion phenotypes in <i>Saccharomyces cerevisiae</i>Cited by: 40
Author(s): Marco Galardini, Bede P. Busby, Cristina Viéitez, Alistair S. Dunham, Athanasios Typas, Pedro Beltrão
Software Mentions: 7
Published: almost 5 years ago
10.1186/s12859-021-04198-1
Comparative evaluation of full-length isoform quantification from RNA-SeqCited by: 12
Author(s): Dimitra Sarantopoulou, Thomas G. Brooks, Soumyashant Nayak, Antonijo Mrčela, Nicholas F. Lahens, Gregory R. Grant
Software Mentions: 7
Published: over 3 years ago
10.1093/bfgp/ely003
The impact of single-cell RNA sequencing on understanding the functional organization of the immune systemCited by: 15
Author(s): Péter Végh, Muzlifah Haniffa
Software Mentions: 7
Published: over 6 years ago
10.1128/mBio.00905-21
Functional and Comparative Analysis of Centromeres Reveals Clade-Specific Genome Rearrangements in <i>Candida auris</i> and a Chromosome Number Change in Related SpeciesCited by: 10
Author(s): Aswathy Narayanan, Rakesh Netha Vadnala, Promit Ganguly, Pavitra Selvakumar, Shivaprakash M Rudramurthy, Rajendra Prasad, Arunaloke Chakrabarti, Rahul Siddharthan, Kaustuv Sanyal
Software Mentions: 7
Published: over 3 years ago
10.3389/fgene.2021.722981
Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq DataCited by: 6
Author(s): Jing Li, Urminder Singh, Zebulun Arendsee, Eve Syrkin Wurtele
Software Mentions: 7
Published: over 3 years ago
10.1186/s12864-021-07488-3
Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIPCited by: 7
Author(s): Thomas M. Adams, Tjelvar S. G. Olsson, Ricardo H. Ramírez-González, Ruth Bryant, R. J. Bryson, Pablo E. Campos, Paul Fenwick, David Feuerhelm, Charlotte Hayes, Tina Henriksson, Amelia Hubbard, Radivoje Jevtić, Christopher Judge, Matthew Kerton, Jean-Luc Da Lage, Clare M. Lewis, Christine Lilly, Udi Meidan, Dario Novoselović, Colin Patrick, R. Wanyera, Diane G. O. Saunders
Software Mentions: 7
Published: over 3 years ago
10.3390/jof7090700
Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by FungiCited by: 3
Author(s): Grace N. Ijoma, Sylvie M Heri, Tonderayi Matambo, Memory Tekere
Software Mentions: 7
Published: about 3 years ago
10.1186/s13059-016-0940-1
A benchmark for RNA-seq quantification pipelinesCited by: 146
Author(s): Mingxiang Teng, Michael I. Love, Carrie A. Davis, Sarah Djebali, Alexander Dobin, Brenton R. Graveley, Sheng Li, Christopher E. Mason, Sara Olson, Dmitri D. Pervouchine, Cricket A. Sloan, Xintao Wei, Lijun Zhan, Rafael A. Irizarry
Software Mentions: 7
Published: over 8 years ago
10.1038/s41597-021-00809-x
A multi-center cross-platform single-cell RNA sequencing reference datasetCited by: 14
Author(s): Xin Chen, Zujun Yang, Wanqiu Chen, Yongmei Zhao, Andrew Farmer, Bao Tran, Vyacheslav Furtak, Malcolm Moos, Wenming Xiao, Charles Wang
Software Mentions: 7
Published: almost 4 years ago
10.1016/j.ebiom.2021.103390
AI-guided discovery of the invariant host response to viral pandemicsCited by: 31
Author(s): Debashis Sahoo, Gajanan D. Katkar, Soni Khandelwal, Mahdi Behroozikhah, Amanraj Claire, Vanessa Castillo, Courtney Tindle, MacKenzie Fuller, Sahar Taheri, Thomas F. Rogers, Nathan Beutler, Sydney I. Ramirez, Stephen A. Rawlings, Victor Pretorius, Davey M Smith, Dennis R. Burton, Laura E. Crotty Alexander, Jason Duran, Shane Crotty, Jennifer M. Dan, Soumita Das, Pradipta Ghosh
Software Mentions: 7
Published: over 3 years ago
10.1371/journal.pgen.1008375
DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary historiesCited by: 29
Author(s): Sheila Lutz, Christian Brion, Margaret Kliebhan, Frank W. Albert
Software Mentions: 7
Published: about 5 years ago
10.1186/s13062-016-0169-7
Sensitivity, specificity, and reproducibility of RNA-Seq differential expression callsCited by: 26
Author(s): Paweł P. Łabaj, David P. Kreil
Software Mentions: 7
Published: almost 8 years ago
10.1186/s13007-021-00791-w
Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell cultureCited by: 3
Author(s): Amir Mahboubi, Nicolas Delhomme, Sara Lea Häggström, Johannes Hanson
Software Mentions: 7
Published: about 3 years ago
10.12688/f1000research.17916.1
Relative Abundance of Transcripts (RATs): Identifying differential isoform abundance from RNA-seqCited by: 19
Author(s): Kimon Froussios, Kira Mourão, Gordon G. Simpson, Geoffrey J. Barton, Nicholas J. Schurch
Software Mentions: 7
Published: over 5 years ago
10.3389/fimmu.2021.568729
Evolution and Expression of the Immune System of a Facultatively Anadromous SalmonidCited by: 7
Author(s): Thomas J. Colgan, Peter Moran, Louise C. Archer, Robert Wynne, Stephen A. Hutton, Philip McGinnity, Thomas E. Reed
Software Mentions: 7
Published: over 3 years ago
10.7554/eLife.56523
DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitorsCited by: 25
Author(s): Maria M. Mikedis, Yuting Fan, Peter K. Nicholls, Toshihiko Endo, Emily Jackson, Sarah A. Cobb, Dirk G. de Rooij, David C. Page
Software Mentions: 7
Published: over 4 years ago
10.7554/eLife.41815
Immune genes are hotspots of shared positive selection across birds and mammalsCited by: 109
Author(s): Allison J. Shultz, Timothy B. Sackton
Software Mentions: 7
Published: almost 6 years ago
10.1186/s12967-021-02936-w
TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models RepositoryCited by: 114
Author(s): Yingdong Zhao, Ming-Chung Li, Mariam M. Konaté, Li Chen, Biswajit Das, Chris Karlovich, P. Mickey Williams, Yvonne A. Evrard, James H. Doroshow, Lisa M. McShane
Software Mentions: 7
Published: over 3 years ago
10.1186/s13059-020-1945-3
Protein velocity and acceleration from single-cell multiomics experimentsCited by: 43
Author(s): Gennady Gorin, Valentine Svensson, Lior Pachter
Software Mentions: 7
Published: almost 5 years ago
10.1186/s12859-017-1942-z
A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativaCited by: 17
Author(s): Megan J. Bowman, Jane A. Pulman, Tiffany L. Liu, Kevin L. Childs
Software Mentions: 7
Published: almost 7 years ago
10.3389/fnmol.2021.680280
Impaired SNF2L Chromatin Remodeling Prolongs Accessibility at Promoters Enriched for Fos/Jun Binding Sites and Delays Granule Neuron DifferentiationCited by: 1
Author(s): Laura Rose Goodwin, Gerardo Zapata, Sara Timpano, Jacob Marenger, David J. Picketts
Software Mentions: 7
Published: over 3 years ago
10.1038/s42003-021-02440-3
Tumor-derived NKG2D ligand sMIC reprograms NK cells to an inflammatory phenotype through CBM signalosome activationCited by: 7
Author(s): Payal Dhar, Fahmin Basher, Zhe Ji, Lei Huang, Si Qin, Derek A. Wainwright, Jerid W. Robinson, Shaye Hagler, Jing Zhou, Sean Mackay, Jennifer D. Wu
Software Mentions: 7
Published: over 3 years ago
10.1002/1878-0261.12389
Using microarray‐based subtyping methods for breast cancer in the era of high‐throughput RNA sequencingCited by: 6
Author(s): Christina Bligaard Pedersen, Finn C. Nielsen, Maria Rossing, Lars Rønn Olsen
Software Mentions: 7
Published: about 6 years ago
10.1186/s12859-019-2852-z
Differential analysis of combinatorial protein complexes with CompleXChangeCited by: 4
Author(s): Thorsten Will, Volkhard Helms
Software Mentions: 7
Published: over 5 years ago
10.1371/journal.pone.0232646
Two-step mixed model approach to analyzing differential alternative RNA splicingCited by: 0
Author(s): Li Luo, Huining Kang, Xichen Li, Scott A. Ness, Christine A. Stidley
Software Mentions: 7
Published: about 4 years ago
10.1186/s12864-021-07443-2
Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencingCited by: 12
Author(s): Carolina P. Moraleda, Diego Robledo, Alejandro P. Gutiérrez, Jorge Del‐Pozo, José M. Yáñez, Ross D. Houston
Software Mentions: 6
Published: over 3 years ago
10.1128/mSystems.00329-20
Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarumCited by: 8
Author(s): Adrián López García de Lomana, Ulrike Kusebauch, Arjun V. Raman, Min Pan, Serdar Turkarslan, Alan Péricles Rodrigues Lorenzetti, Robert L. Moritz, Nitin S. Baliga
Software Mentions: 6
Published: about 4 years ago
10.1093/femsyr/foaa044
Pseudohyphal differentiation in Komagataella phaffii: investigating the FLO gene familyCited by: 3
Author(s): Sonakshi De, Corinna Rebnegger, Josef W. Moser, Nadine E Tatto, Alexandra B. Graf, Diethard Mattanovich, Brigitte Gasser
Software Mentions: 6
Published: over 4 years ago
10.1128/mBio.02146-20
Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore SystemCited by: 20
Author(s): Charlotte B. Francoeur, Lily Khadempour, Rolando D. Moreira-Soto, Kirsten Gotting, Adam J. Book, Adrián A. Pinto‐Tomás, Ken Keefover‐Ring, Cameron R. Currie
Software Mentions: 6
Published: about 4 years ago
10.1186/s12859-016-1195-2
A fuzzy method for RNA-Seq differential expression analysis in presence of multireadsCited by: 16
Author(s): Arianna Consiglio, Corrado Mencar, Giorgio Grillo, Flaviana Marzano, Mariano Francesco Caratozzolo, Sabino Liuni
Software Mentions: 6
Published: about 8 years ago
10.12688/f1000research.11355.2
Arkas: Rapid reproducible RNAseq analysisCited by: 9
Author(s): Anthony Colombo, Timothy J. Triche, Giridharan Ramsingh
Software Mentions: 6
Published: over 7 years ago
10.1186/s13059-018-1419-z
Gene-level differential analysis at transcript-level resolutionCited by: 97
Author(s): Lynn Yi, Harold Pimentel, Nicolas Bray, Lior Pachter
Software Mentions: 6
Published: over 6 years ago
10.26508/lsa.201800175
A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogsCited by: 16
Author(s): Charlotte Soneson, Michael I. Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, Mark D. Robinson
Software Mentions: 6
Published: almost 6 years ago
10.1371/journal.pgen.1007788
Single-cell RNA-sequencing reveals transcriptional dynamics of estrogen-induced dysplasia in the ovarian surface epitheliumCited by: 16
Author(s): Nhung Vuong, David P. Cook, Laura A. Forrest, Lauren E. Carter, Pascale Robineau-Charette, Joshua M. Kofsky, Kendra M. Hodgkinson, Barbara C. Vanderhyden
Software Mentions: 6
Published: about 6 years ago
10.1186/s13287-020-01983-2
IRF-1 expressed in the inner cell mass of the porcine early blastocyst enhances the pluripotency of induced pluripotent stem cellsCited by: 8
Author(s): Bingbo Shi, Dengfeng Gao, Zhong Liu, Minglei Zhi, Xiaogang Weng, Junjun Xu, Junhong Li, Xuguang Du, Yanli Xin, Jie Gao, Qianqian Zhu, Suying Cao, Liu Z
Software Mentions: 6
Published: almost 4 years ago
10.1002/ece3.5516
Extensive genetic differentiation between recently evolved sympatric Arctic charr morphsCited by: 18
Author(s): Jóhannes Guðbrandsson, Kalina H. Kapralova, Sigríður Rut Franzdóttir, Þóra Margrét Bergsveinsdóttir, Völundur Hafstað, Zophonı́as O. Jónsson, Sigurður S. Snorrason, Arnar Pálsson
Software Mentions: 6
Published: about 5 years ago
10.1371/journal.pgen.1008804
Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertilityCited by: 24
Author(s): Maya Hiltpold, Guanglin Niu, Naveen Kumar Kadri, Danang Crysnanto, Zih-Hua Fang, Mirjam Spengeler, F. Schmitz‐Hsu, Christian Fuerst, Hermann Schwarzenbacher, Franz R. Seefried, Frauke Seehusen, Ulrich Witschi, Angelika Schnieke, R. Fries, Heinrich Bollwein, Krzysztof Flisikowski, Hubert Pausch
Software Mentions: 6
Published: over 4 years ago
10.15252/embj.2020107100
<i>De novo</i> DNA methylation controls neuronal maturation during adult hippocampal neurogenesisCited by: 17
Author(s): Sara Zocher, Rupert W. Overall, Gabriel Berdugo-Vega, Nicole Rund, Anne Karasinsky, Vijay S. Adusumilli, Christina Steinhauer, Sina Scheibenstock, Kristian Händler, Joachim L. Schultze, Federico Calegari, Gerd Kempermann
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pcbi.1007162
Cross-species functional modules link proteostasis to human normal agingCited by: 10
Author(s): Andrea Komljenović, Hao Li, Vincenzo Sorrentino, Zoltán Kutalik, Johan Auwerx, Marc Robinson‐Rechavi
Software Mentions: 6
Published: over 5 years ago
10.1093/database/bay014
TransAtlasDB: an integrated database connecting expression data, metadata and variantsCited by: 2
Author(s): Modupeore O. Adetunji, Susan J. Lamont, Carl J. Schmidt
Software Mentions: 6
Published: almost 7 years ago
10.3390/genes11040428
LSTrAP-Cloud: A User-Friendly Cloud Computing Pipeline to Infer Coexpression NetworksCited by: 9
Author(s): Qiao Wen Tan, Wooi-Boon Goh, Marek Mutwil
Software Mentions: 6
Published: over 4 years ago
10.3390/genes11121500
Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in CucumisCited by: 7
Author(s): Panqiao Wang, Xiaqing Yu, Zhanguo Zhu, Yufei Zhai, Qinzheng Zhao, Meng Yang, Ji Li, Qunfeng Lou, Jinfeng Chen
Software Mentions: 6
Published: almost 4 years ago
10.3390/genes11121487
RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using NextflowCited by: 13
Author(s): Marie Lataretu, Martin Hölzer
Software Mentions: 6
Published: almost 4 years ago
10.1186/s12864-021-07930-6
Choice of pre-processing pipeline influences clustering quality of scRNA-seq datasetsCited by: 4
Author(s): Inbal Shainer, Manuel Stemmer
Software Mentions: 6
Published: about 3 years ago
10.1038/s42003-020-0916-2
Tankyrase inhibition sensitizes melanoma to PD-1 immune checkpoint blockade in syngeneic mouse modelsCited by: 23
Author(s): Jo Waaler, Line Mygland, Anders Aune Tveita, Martin Frank Strand, Nina Solberg, Petter Olsen, Aleksandra Aizenshtadt, Marte Fauskanger, Kaja Lund, Jo Waaler, Max Lycke, Elisabeth Dybing, Vegard Nygaard, Sigurd Leinæs Bøe, Karen‐Marie Heintz, Eivind Hovig, Clara Hammarström, Alexandre Corthay, Stefan Krauß
Software Mentions: 6
Published: over 4 years ago
10.1186/s13059-020-01967-8
BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertaintyCited by: 16
Author(s): Simone Tiberi, Mark D. Robinson
Software Mentions: 6
Published: over 4 years ago
10.1186/s13072-017-0144-2
Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential functionCited by: 19
Author(s): Christopher Schröder, Elsa Leitão, Stefan Wallner, Gerd Schmitz, Ludger Klein‐Hitpass, Anupam Sinha, Karl‐Heinz Jöckel, Markus M. Nöthen, Per Hoffmann, Markus M. Nöthen, Michael Steffens, Peter Ebert, Sven Rahmann, Bernhard Horsthemke
Software Mentions: 6
Published: over 7 years ago
10.1038/s41598-020-80111-9
FAK regulates IL-33 expression by controlling chromatin accessibility at c-Jun motifsCited by: 13
Author(s): Billie G. C. Griffith, Rosanna Upstill-Goddard, Holly Brunton, Graeme R. Grimes, Andrew V. Biankin, Bryan Serrels, Adam Byron, Margaret C. Frame
Software Mentions: 6
Published: almost 4 years ago
10.1186/s13024-020-00415-2
Diabetic phenotype in mouse and humans reduces the number of microglia around β-amyloid plaquesCited by: 16
Author(s): Teemu Natunen, Henna Martiskainen, Mikael Marttinen, Sami Gabbouj, Hennariikka Koivisto, Susanna Kemppainen, Satu Kaipainen, Mari Takalo, Hélèna Svobodova, Luukas Leppänen, Benjam Kemiläinen, Simo Ryhänen, Teemu Kuulasmaa, Eija Rahunen, Sisko Juutinen, Petra Mäkinen, Pasi Miettinen, Tuomas Rauramaa, Jussi Pihlajamäki, Annakaisa Haapasalo, Ville Leinonen, Heikki Tanila, Mikko Hiltunen
Software Mentions: 5
Published: about 4 years ago
10.1371/journal.pone.0201483
HSRA: Hadoop-based spliced read aligner for RNA sequencing dataCited by: 11
Author(s): Roberto R. Expósito, Jorge González-Domínguez, Juan Touriño
Software Mentions: 5
Published: over 6 years ago
10.1186/s13229-020-00359-w
IGF-1 treatment causes unique transcriptional response in neurons from individuals with idiopathic autismCited by: 17
Author(s): Sara B. Linker, Ana Paula Mendes, Maria C. Marchetto
Software Mentions: 5
Published: over 4 years ago
10.1186/s12263-021-00688-2
An 8-week freeze-dried blueberry supplement impacts immune-related pathways: a randomized, double-blind placebo-controlled trialCited by: 7
Author(s): Michèle Rousseau, Justine Horne, Frédéric Guénard, Juan de Toro‐Martín, Véronique Garneau, Valérie Guay, Michèle Kearney, Geneviève Pilon, Denis Roy, Patrick Couture, Charles Couillard, André Marette
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pgen.1006619
Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticumCited by: 46
Author(s): Yi Jin Liew, Yong Li, Sebastian Baumgarten, Christian R. Voolstra, Manuel Aranda
Software Mentions: 5
Published: over 7 years ago
10.1371/journal.pgen.1009213
Gene regulatory effects of a large chromosomal inversion in highland maizeCited by: 38
Author(s): Taylor M. Crow, James Ta, Saghi Nojoomi, M. Rocío Aguilar-Rangel, Jorge Vladimir Torres Rodríguez, David M. Gates, Rubén Rellán‐Álvarez, Ruairidh J. H. Sawers, Daniel E. Runcie
Software Mentions: 5
Published: almost 4 years ago
10.1002/ece3.6422
Evidence of capacitation in the parasitoid wasp, Nasonia vitripennis, and its potential role in sex allocationCited by: 0
Author(s): Alun R. C. Jones, Eamonn B. Mallon
Software Mentions: 5
Published: over 4 years ago
10.3389/fonc.2020.01195
Multi-Omics Characterization of the 4T1 Murine Mammary Gland Tumor ModelCited by: 82
Author(s): Barbara Schrörs, Sebastian Boegel, Christian Albrecht, Thomas Bukur, Valesca Bukur, Christoph Holtsträter, Christoph Ritzel, Katja Manninen, Arbel D. Tadmor, Mathias Vormehr, Uğur Şahin, Martin Löwer
Software Mentions: 5
Published: over 4 years ago
10.1371/journal.ppat.1008346
Host-derived circular RNAs display proviral activities in Hepatitis C virus-infected cellsCited by: 28
Author(s): Tzu‐Chun Chen, Marc Talló-Parra, Qian M. Cao, Sebastián Kadener, René Böttcher, Gemma Pérez‐Vilaró, Pakpoom Boonchuen, Kunlaya Somboonwiwat, Juana Díez, Peter Sarnow
Software Mentions: 5
Published: over 4 years ago
10.3390/plants9091176
Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic ProfilingCited by: 19
Author(s): Ivan Tsers, Vladimir Gorshkov, Natalia Gogoleva, Olga Parfirova, Olga Petrova, Alexander A. Kamnev
Software Mentions: 5
Published: about 4 years ago
10.3390/biology10010039
Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq DatasetsCited by: 11
Author(s): Adeel Malik, Chang-Bae Kim
Software Mentions: 5
Published: almost 4 years ago
10.1371/journal.ppat.1009217
EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escapeCited by: 14
Author(s): Nathan Ungerleider, Whitney Bullard, Mehmet Kara, Xia Wang, Claire Roberts, Rolf Renne, Scott A. Tibbetts, Erik K. Flemington
Software Mentions: 5
Published: over 3 years ago
10.1038/s41598-020-78288-0
Common and personal target genes of the micronutrient vitamin D in primary immune cells from human peripheral bloodCited by: 19
Author(s): Andrea Hanel, Antonio Neme, Marjo Malinen, Emmi Hämäläinen, Henna-Riikka Malmberg, Stéphane Etheve, Tomi‐Pekka Tuomainen, Jyrki K. Virtanen, Igor Bendik, Carsten Carlberg
Software Mentions: 5
Published: almost 4 years ago
10.1111/tpj.14699
Heating quinoa shoots results in yield loss by inhibiting fruit production and delaying maturityCited by: 18
Author(s): Jose C. Tovar, Carlos Quillatupa, Steven T. Callen, S. Elizabeth Castillo, Paige Pearson, Anastasia Shamin, Haley Schuhl, Noah Fahlgren
Software Mentions: 5
Published: over 4 years ago
10.1002/ps.6061
Toxicological and molecular profiling of insecticide resistance in a Brazilian strain of fall armyworm resistant to Bt Cry1 proteinsCited by: 24
Author(s): Debora Boaventura, Benjamin Buer, Niklas Hamaekers, Frank Maiwald, Ralf Nauen
Software Mentions: 5
Published: about 4 years ago